I have been breeding rats for over 10 years now and I will tell you this: Rats usually do not eat their young unless one of two things is wrong:
1) She is starving and can't get enough food (which doesn't sound like it's the case here), and
2) There was something seriously wrong with the babies, the mother knew they wouldn't survive and so she replenished her lost protein by consuming them.
It is definitely possible that something went wrong with her pregnancy and that the pups who are "gone" were not all right. The mother knew this and took matters into her own hands to get rid of them. It is very likely that the problem is with her and I would NOT breed her again at all. I would say either retire her (if you keep them) or feed her off (if you don't).
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